module Array = ArrayLabels
module List = ListLabels
+module StrSet = Set.Make(String)
+module Unix = UnixLabels
+
+module Metrics : sig
+ type t
+
+ val init
+ : unit -> t
+ val report
+ : t
+ -> wall_time_all:float
+ -> wall_time_group_by_size:float
+ -> wall_time_group_by_head:float
+ -> wall_time_group_by_digest:float
+ -> proc_time_all:float
+ -> proc_time_group_by_size:float
+ -> proc_time_group_by_head:float
+ -> proc_time_group_by_digest:float
+ -> unit
+
+ val file_considered
+ : t -> size:int -> unit
+ val file_ignored
+ : t -> size:int -> unit
+ val file_empty
+ : t -> unit
+ val file_sampled
+ : t -> unit
+ val chunk_read
+ : t -> size:int -> unit
+ val file_unique_size
+ : t -> size:int -> unit
+ val file_unique_sample
+ : t -> size:int -> unit
+ val file_hashed
+ : t -> size:int -> unit
+ val digest
+ : t -> unit
+ val redundant_data
+ : t -> size:int -> unit
+end = struct
+ type t =
+ { considered_files : int ref
+ ; considered_bytes : int ref
+ ; empty : int ref
+ ; ignored_files : int ref
+ ; ignored_bytes : int ref
+ ; unique_size_files : int ref
+ ; unique_size_bytes : int ref
+ ; unique_sample_files : int ref
+ ; unique_sample_bytes : int ref
+ ; sampled_files : int ref
+ ; sampled_bytes : int ref
+ ; hashed_files : int ref
+ ; hashed_bytes : int ref
+ ; digests : int ref
+ ; redundant_data : int ref
+ }
+
+ let init () =
+ { considered_files = ref 0
+ ; considered_bytes = ref 0
+ ; empty = ref 0
+ ; ignored_files = ref 0
+ ; ignored_bytes = ref 0
+ ; unique_size_files = ref 0
+ ; unique_size_bytes = ref 0
+ ; sampled_files = ref 0
+ ; sampled_bytes = ref 0
+ ; hashed_files = ref 0
+ ; hashed_bytes = ref 0
+ ; unique_sample_files = ref 0
+ ; unique_sample_bytes = ref 0
+ ; digests = ref 0
+ ; redundant_data = ref 0
+ }
+
+ let add sum addend =
+ sum := !sum + addend
+
+ let file_considered t ~size =
+ incr t.considered_files;
+ add t.considered_bytes size
+
+ let file_ignored {ignored_files; ignored_bytes; _} ~size =
+ incr ignored_files;
+ add ignored_bytes size
+
+ let file_empty t =
+ incr t.empty
+
+ let chunk_read t ~size =
+ add t.sampled_bytes size
+
+ let file_sampled t =
+ incr t.sampled_files
+
+ let file_unique_size t ~size =
+ incr t.unique_size_files;
+ add t.unique_size_bytes size
+
+ let file_unique_sample t ~size =
+ incr t.unique_sample_files;
+ add t.unique_sample_bytes size
+
+ let file_hashed t ~size =
+ incr t.hashed_files;
+ add t.hashed_bytes size
+
+ let digest t =
+ incr t.digests
+
+ let redundant_data t ~size =
+ add t.redundant_data size
+
+ let report
+ t
+ ~wall_time_all
+ ~wall_time_group_by_size
+ ~wall_time_group_by_head
+ ~wall_time_group_by_digest
+ ~proc_time_all
+ ~proc_time_group_by_size
+ ~proc_time_group_by_head
+ ~proc_time_group_by_digest
+ =
+ let b_to_mb b = (float_of_int b) /. 1024. /. 1024. in
+ let b_to_gb b = (b_to_mb b) /. 1024. in
+ eprintf "Total time : %.2f wall sec %.2f proc sec\n%!"
+ wall_time_all
+ proc_time_all;
+ eprintf "Considered : %8d files %6.2f Gb\n%!"
+ !(t.considered_files)
+ (b_to_gb !(t.considered_bytes));
+ eprintf "Sampled : %8d files %6.2f Gb\n%!"
+ !(t.sampled_files)
+ (b_to_gb !(t.sampled_bytes));
+ eprintf "Hashed : %8d files %6.2f Gb %6.2f wall sec %6.2f proc sec\n%!"
+ !(t.hashed_files)
+ (b_to_gb !(t.hashed_bytes))
+ wall_time_group_by_digest
+ proc_time_group_by_digest;
+ eprintf "Digests : %8d\n%!"
+ !(t.digests);
+ eprintf "Duplicates (Hashed - Digests): %8d files %6.2f Gb\n%!"
+ (!(t.hashed_files) - !(t.digests))
+ (b_to_gb !(t.redundant_data));
+ eprintf "Skipped due to 0 size : %8d files\n%!" !(t.empty);
+ eprintf "Skipped due to unique size : %8d files %6.2f Gb %6.2f wall sec %6.2f proc sec\n%!"
+ !(t.unique_size_files)
+ (b_to_gb !(t.unique_size_bytes))
+ wall_time_group_by_size
+ proc_time_group_by_size;
+ eprintf "Skipped due to unique sample : %8d files %6.2f Gb %6.2f wall sec %6.2f proc sec\n%!"
+ !(t.unique_sample_files)
+ (b_to_gb !(t.unique_sample_bytes))
+ wall_time_group_by_head
+ proc_time_group_by_head;
+ eprintf "Ignored due to regex match : %8d files %6.2f Gb\n%!"
+ !(t.ignored_files)
+ (b_to_gb !(t.ignored_bytes))
+end
+
+module M = Metrics
module Stream : sig
type 'a t
val create : (unit -> 'a option) -> 'a t
+ val of_queue : 'a Queue.t -> 'a t
+
val iter : 'a t -> f:('a -> unit) -> unit
+
+ val bag_map : 'a t -> njobs:int -> f:('a -> 'b) -> ('a * 'b) t
+ (** Parallel map with arbitrarily-reordered elements. *)
+
+ val map : 'a t -> f:('a -> 'b) -> 'b t
+
+ val filter : 'a t -> f:('a -> bool) -> 'a t
+
+ val concat : ('a t) list -> 'a t
+
+ val group_by : 'a t -> f:('a -> 'b) -> ('b * int * 'a list) t
end = struct
module S = Stream
type 'a t =
- 'a S.t
+ {mutable streams : ('a S.t) list}
+
+ type ('input, 'output) msg_from_vassal =
+ | Ready of int
+ | Result of (int * ('input * 'output))
+ | Exiting of int
+
+ type 'input msg_from_lord =
+ | Job of 'input option
let create f =
- S.from (fun _ -> f ())
+ {streams = [S.from (fun _ -> f ())]}
+
+ let of_queue q =
+ create (fun () ->
+ match Queue.take q with
+ | exception Queue.Empty ->
+ None
+ | x ->
+ Some x
+ )
+
+ let rec next t =
+ match t.streams with
+ | [] ->
+ None
+ | s :: streams ->
+ (match S.next s with
+ | exception Stream.Failure ->
+ t.streams <- streams;
+ next t
+ | x ->
+ Some x
+ )
+
+ let map t ~f =
+ create (fun () ->
+ match next t with
+ | None -> None
+ | Some x -> Some (f x)
+ )
+
+ let filter t ~f =
+ let rec filter () =
+ match next t with
+ | None ->
+ None
+ | Some x when f x ->
+ Some x
+ | Some _ ->
+ filter ()
+ in
+ create filter
let iter t ~f =
- S.iter f t
+ List.iter t.streams ~f:(S.iter f)
+
+ let concat ts =
+ {streams = List.concat (List.map ts ~f:(fun {streams} -> streams))}
+
+ let group_by t ~f =
+ let groups_tbl = Hashtbl.create 1_000_000 in
+ let group_update x =
+ let group = f x in
+ let members =
+ match Hashtbl.find_opt groups_tbl group with
+ | None ->
+ (1, [x])
+ | Some (n, xs) ->
+ (succ n, x :: xs)
+ in
+ Hashtbl.replace groups_tbl group members
+ in
+ iter t ~f:group_update;
+ let groups = Queue.create () in
+ Hashtbl.iter
+ (fun name (length, members) -> Queue.add (name, length, members) groups)
+ groups_tbl;
+ of_queue groups
+
+ module Ipc : sig
+ val send : out_channel -> 'a -> unit
+ val recv : in_channel -> 'a
+ end = struct
+ let send oc msg =
+ Marshal.to_channel oc msg [];
+ flush oc
+
+ let recv ic =
+ Marshal.from_channel ic
+ end
+
+ let lord t ~njobs ~vassals ~ic ~ocs =
+ let active_vassals = ref njobs in
+ let results = Queue.create () in
+ let rec loop () =
+ match ((Ipc.recv ic) : ('input, 'output) msg_from_vassal) with
+ | Exiting i ->
+ close_out ocs.(i);
+ decr active_vassals;
+ if !active_vassals = 0 then () else loop ()
+ | Ready i ->
+ Ipc.send ocs.(i) (Job (next t));
+ loop ()
+ | Result (i, result) ->
+ Queue.add result results;
+ Ipc.send ocs.(i) (Job (next t));
+ loop ()
+ in
+ let rec wait = function
+ | [] ->
+ ()
+ | vassals ->
+ let pid, _process_status = Unix.wait () in
+ (* TODO: handle process_status *)
+ wait (List.filter vassals ~f:(fun p -> p <> pid))
+ in
+ loop ();
+ close_in ic;
+ wait vassals;
+ of_queue results
+
+ let vassal i ~f ~vassal_pipe_r ~lord_pipe_w =
+ let ic = Unix.in_channel_of_descr vassal_pipe_r in
+ let oc = Unix.out_channel_of_descr lord_pipe_w in
+ let rec loop () =
+ match (Ipc.recv ic : 'input msg_from_lord) with
+ | Job (Some x) ->
+ Ipc.send oc (Result (i, (x, f x)));
+ loop ()
+ | Job None ->
+ Ipc.send oc (Exiting i)
+ in
+ Ipc.send oc (Ready i);
+ loop ();
+ close_in ic;
+ close_out oc;
+ exit 0
+
+ let bag_map t ~njobs ~f =
+ let lord_pipe_r, lord_pipe_w = Unix.pipe () in
+ let vassal_pipes = Array.init njobs ~f:(fun _ -> Unix.pipe ()) in
+ let vassal_pipes_r = Array.map vassal_pipes ~f:(fun (r, _) -> r) in
+ let vassal_pipes_w = Array.map vassal_pipes ~f:(fun (_, w) -> w) in
+ let vassals = ref [] in
+ for i=0 to (njobs - 1) do
+ begin match Unix.fork () with
+ | 0 ->
+ Unix.close lord_pipe_r;
+ vassal i ~f ~lord_pipe_w ~vassal_pipe_r:vassal_pipes_r.(i)
+ | pid ->
+ vassals := pid :: !vassals
+ end
+ done;
+ Unix.close lord_pipe_w;
+ lord
+ t
+ ~njobs
+ ~vassals:!vassals
+ ~ic:(Unix.in_channel_of_descr lord_pipe_r)
+ ~ocs:(Array.map vassal_pipes_w ~f:Unix.out_channel_of_descr)
end
module In_channel : sig
)
end
-module Directory_tree : sig
- val find_files : string -> string Stream.t
+module File : sig
+ type t =
+ { path : string
+ ; size : int
+ }
+
+ val find : string -> t Stream.t
+ (** Find all files in the directory tree, starting from the given root path *)
+
+ val lookup : string Stream.t -> t Stream.t
+ (** Lookup file info for given paths *)
+
+ val head : t -> len:int -> metrics:M.t -> string
+
+ val filter_out_unique_sizes : t Stream.t -> metrics:M.t -> t Stream.t
+ val filter_out_unique_heads : t Stream.t -> len:int -> metrics:M.t -> t Stream.t
end = struct
- let find_files root =
+ type t =
+ { path : string
+ ; size : int
+ }
+
+ let lookup paths =
+ Stream.map paths ~f:(fun path ->
+ let {Unix.st_size = size; _} = Unix.lstat path in
+ {path; size}
+ )
+
+ let find root =
let dirs = Queue.create () in
let files = Queue.create () in
let explore parent =
Array.iter (Sys.readdir parent) ~f:(fun child ->
let path = Filename.concat parent child in
- let {Unix.st_kind = file_kind; _} = Unix.lstat path in
+ let {Unix.st_kind = file_kind; st_size; _} = Unix.lstat path in
match file_kind with
| Unix.S_REG ->
- Queue.add path files
+ let file = {path; size = st_size} in
+ Queue.add file files
| Unix.S_DIR ->
Queue.add path dirs
| Unix.S_CHR
next ()
in
Stream.create next
+
+ let filter_out_singletons files ~group ~handle_singleton =
+ let q = Queue.create () in
+ Stream.iter (Stream.group_by files ~f:group) ~f:(fun group ->
+ let (_, n, members) = group in
+ if n > 1 then
+ List.iter members ~f:(fun m -> Queue.add m q)
+ else
+ handle_singleton group
+ );
+ Stream.of_queue q
+
+ let filter_out_unique_sizes files ~metrics =
+ filter_out_singletons
+ files
+ ~group:(fun {size; _} -> size)
+ ~handle_singleton:(fun (size, _, _) -> M.file_unique_size metrics ~size)
+
+ let head {path; _} ~len ~metrics =
+ M.file_sampled metrics;
+ let buf = Bytes.make len ' ' in
+ let ic = open_in_bin path in
+ let rec read pos len =
+ assert (len >= 0);
+ if len = 0 then
+ ()
+ else begin
+ let chunk_size = input ic buf pos len in
+ M.chunk_read metrics ~size:chunk_size;
+ if chunk_size = 0 then (* EOF *)
+ ()
+ else
+ read (pos + chunk_size) (len - chunk_size)
+ end
+ in
+ read 0 len;
+ close_in ic;
+ Bytes.to_string buf
+
+ let filter_out_unique_heads files ~len ~metrics =
+ filter_out_singletons
+ files
+ ~group:(head ~len ~metrics)
+ ~handle_singleton:(fun (_, _, files) ->
+ let {size; _} = List.hd files in (* Guaranteed non-empty *)
+ M.file_unique_sample metrics ~size
+ )
end
type input =
- | Root_path of string
- | Paths_on_stdin
+ | Stdin
+ | Directories of string list
+
+type output =
+ | Stdout
+ | Directory of string
+
+type opt =
+ { input : input
+ ; output : output
+ ; ignore : string -> bool
+ ; sample : int
+ ; njobs : int
+ }
-let main input =
- let paths =
+let make_input_stream input ignore ~metrics =
+ let input =
match input with
- | Paths_on_stdin -> In_channel.lines stdin
- | Root_path root -> Directory_tree.find_files root
+ | Stdin ->
+ File.lookup (In_channel.lines stdin)
+ | Directories paths ->
+ let paths = StrSet.elements (StrSet.of_list paths) in
+ Stream.concat (List.map paths ~f:File.find)
in
- let paths_by_digest = Hashtbl.create 1_000_000 in
- let path_count = ref 0 in
- let t0 = Sys.time () in
- Stream.iter paths ~f:(fun path ->
- incr path_count;
- try
- let digest = Digest.file path in
- let paths =
- match Hashtbl.find_opt paths_by_digest digest with
- | None ->
- []
- | Some paths ->
- paths
+ Stream.filter input ~f:(fun {File.path; size} ->
+ M.file_considered metrics ~size;
+ let empty = size = 0 in
+ let ignored = ignore path in
+ if empty then M.file_empty metrics;
+ if ignored then M.file_ignored metrics ~size;
+ (not empty) && (not ignored)
+ )
+
+let make_output_fun = function
+ | Stdout ->
+ fun digest n_files files ->
+ printf "%s %d\n%!" (Digest.to_hex digest) n_files;
+ List.iter files ~f:(fun {File.path; _} ->
+ printf " %S\n%!" path
+ )
+ | Directory dir ->
+ fun digest _ files ->
+ let digest = Digest.to_hex digest in
+ let dir = Filename.concat dir (String.sub digest 0 2) in
+ Unix.mkdir dir ~perm:0o700;
+ let oc = open_out (Filename.concat dir digest) in
+ List.iter files ~f:(fun {File.path; _} ->
+ output_string oc (sprintf "%S\n%!" path)
+ );
+ close_out oc
+
+let time_wall () =
+ Unix.gettimeofday ()
+
+let time_proc () =
+ Sys.time ()
+
+let main {input; output; ignore; sample = sample_len; njobs} =
+ let wt0_all = time_wall () in
+ let pt0_all = time_proc () in
+ let metrics = M.init () in
+ let output = make_output_fun output in
+ let input = make_input_stream input ignore ~metrics in
+ (* TODO: Make a nice(r) abstraction to re-assemble pieces in the pipeline:
+ *
+ * from input to files_by_size
+ * from files_by_size to files_by_sample
+ * from files_by_sample to files_by_digest
+ * from files_by_digest to output
+ *
+ * input |> files_by_size |> files_by_sample |> files_by_digest |> output
+ *)
+
+ let files = input in
+
+ let wt0_group_by_size = time_wall () in
+ let pt0_group_by_size = time_proc () in
+ eprintf "[debug] filtering-out files with unique size\n%!";
+ let files = File.filter_out_unique_sizes files ~metrics in
+ let pt1_group_by_size = time_proc () in
+ let wt1_group_by_size = time_wall () in
+
+ let wt0_group_by_sample = wt1_group_by_size in
+ let pt0_group_by_sample = pt1_group_by_size in
+ eprintf "[debug] filtering-out files with unique heads\n%!";
+ let files =
+ if njobs > 1 then begin
+ let q = Queue.create () in
+ files
+ |> Stream.bag_map ~njobs ~f:(File.head ~len:sample_len ~metrics)
+ |> Stream.group_by ~f:snd
+ |> Stream.map ~f:(fun (d, n, pairs) -> (d, n, List.map pairs ~f:fst))
+ |> Stream.filter ~f:(fun (_, n, _) -> n > 1)
+ |> Stream.iter ~f:(fun (_, _, fs) -> List.iter fs ~f:(fun f -> Queue.add f q))
+ ;
+ Stream.of_queue q
+ end else
+ File.filter_out_unique_heads files ~len:sample_len ~metrics
+ in
+ let pt1_group_by_sample = time_proc () in
+ let wt1_group_by_sample = time_wall () in
+
+ let wt0_group_by_digest = wt1_group_by_sample in
+ let pt0_group_by_digest = pt1_group_by_sample in
+ eprintf "[debug] hashing\n%!";
+ let groups =
+ if njobs > 1 then
+ let with_digests =
+ Stream.bag_map files ~njobs ~f:(fun {File.path; _} -> Digest.file path)
in
- Hashtbl.replace paths_by_digest digest (path :: paths)
- with Sys_error e ->
- eprintf "WARNING: Failed to process %S: %S\n%!" path e
+ Stream.map (Stream.group_by with_digests ~f:snd) ~f:(
+ fun (digest, n, file_digest_pairs) ->
+ let files =
+ List.map file_digest_pairs ~f:(fun (file, _) ->
+ M.file_hashed metrics ~size:file.File.size;
+ file
+ )
+ in
+ (digest, n, files)
+ )
+ else
+ Stream.group_by files ~f:(fun {File.path; size} ->
+ M.file_hashed metrics ~size;
+ Digest.file path
+ )
+ in
+ let pt1_group_by_digest = time_proc () in
+ let wt1_group_by_digest = time_wall () in
+
+ eprintf "[debug] reporting\n%!";
+ Stream.iter groups ~f:(fun (d, n, files) ->
+ M.digest metrics;
+ if n > 1 then
+ M.redundant_data metrics ~size:(n * (List.hd files).File.size);
+ output d n files
);
- Hashtbl.iter
- (fun digest paths ->
- let n_paths = List.length paths in
- if n_paths > 1 then begin
- printf "%s %d\n%!" (Digest.to_hex digest) n_paths;
- List.iter paths ~f:(fun path -> printf " %s\n%!" path)
- end
- )
- paths_by_digest;
- let t1 = Sys.time () in
- eprintf "Processed %d files in %f seconds.\n%!" !path_count (t1 -. t0)
-let () =
- let input = ref Paths_on_stdin in
+ let pt1_all = time_proc () in
+ let wt1_all = time_wall () in
+
+ M.report metrics
+ ~wall_time_all: (wt1_all -. wt0_all)
+ ~wall_time_group_by_size: (wt1_group_by_size -. wt0_group_by_size)
+ ~wall_time_group_by_head: (wt1_group_by_sample -. wt0_group_by_sample)
+ ~wall_time_group_by_digest:(wt1_group_by_digest -. wt0_group_by_digest)
+ ~proc_time_all: (pt1_all -. pt0_all)
+ ~proc_time_group_by_size: (pt1_group_by_size -. pt0_group_by_size)
+ ~proc_time_group_by_head: (pt1_group_by_sample -. pt0_group_by_sample)
+ ~proc_time_group_by_digest:(pt1_group_by_digest -. pt0_group_by_digest)
+
+let get_opt () : opt =
+ let assert_ test x msg =
+ if not (test x) then begin
+ eprintf "%s\n%!" msg;
+ exit 1
+ end
+ in
+ let assert_file_exists path =
+ assert_ Sys.file_exists path (sprintf "File does not exist: %S" path)
+ in
+ let assert_file_is_dir path =
+ assert_ Sys.is_directory path (sprintf "File is not a directory: %S" path)
+ in
+ let input = ref Stdin in
+ let output = ref Stdout in
+ let ignore = ref (fun _ -> false) in
+ let sample = ref 512 in
+ let njobs = ref 6 in
+ let spec =
+ [ ( "-out"
+ , Arg.String (fun path ->
+ assert_file_exists path;
+ assert_file_is_dir path;
+ output := Directory path
+ )
+ , " Output to this directory instead of stdout."
+ )
+ ; ( "-ignore"
+ , Arg.String (fun regexp ->
+ let regexp = Str.regexp regexp in
+ ignore := fun string -> Str.string_match regexp string 0)
+ , " Ignore file paths which match this regexp pattern (see Str module)."
+ )
+ ; ( "-sample"
+ , Arg.Set_int sample
+ , (sprintf " Byte size of file samples to use. Default: %d" !sample)
+ )
+ ; ( "-j"
+ , Arg.Set_int njobs
+ , (sprintf " Number of parallel jobs. Default: %d" !njobs)
+ )
+ ]
+ in
Arg.parse
- []
- (function
- | path when Sys.file_exists path ->
- input := Root_path path
- | path ->
- eprintf "File does not exist: %S\n%!" path;
- exit 1
+ (Arg.align spec)
+ (fun path ->
+ assert_file_exists path;
+ assert_file_is_dir path;
+ match !input with
+ | Stdin ->
+ input := Directories [path]
+ | Directories paths ->
+ input := Directories (path :: paths)
)
"";
- main !input
+ assert_
+ (fun x -> x > 0)
+ !sample
+ (sprintf "Sample size cannot be negative: %d" !sample);
+ { input = !input
+ ; output = !output
+ ; ignore = !ignore
+ ; sample = !sample
+ ; njobs = !njobs
+ }
+
+let () =
+ main (get_opt ())
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